R.EcoRII

EcoRII (pronounced 'eco R two') is an Restriction endonuclease enzyme (REase) of the restriction modification system (RM) naturally found in Escherichia coli, a Gram-negative bacteria. Its molecular mass is 45.2 kDa, being composed of 402 amino acids.^[1]

Eco RII dimer based on PDB ID 1NA6

Mode of action

EcoRII is a bacterial Type IIE^[2] REase that interacts with two^[3] or three^[4] copies of the pseudopalindromic DNA recognition sequence 5'-CCWGG-3' (W = A or T), one being the actual target of cleavage, the other(s) serving as the allosteric activator(s). EcoRII cuts the target DNA sequence CCWGG, generating sticky ends.^[5]

Cut diagram

Recognition site	Cut results
5' NNCCWGGNN 3' NNGGWCCNN	5' NN CCWGGNN 3' NNGGWCC NN

Structure

Restriction endonuclease EcoRII, N-terminal
crystal structure of restriction endonuclease ecorii mutant r88a
Identifiers
Symbol	EcoRII-N
Pfam	PF09217
Pfam clan	CL0405
InterPro	IPR015300
SCOP2	1na6 / SCOPe / SUPFAM
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

EcoRII C terminal
crystal structure of restriction endonuclease ecorii mutant r88a
Identifiers
Symbol	EcoRII-C
Pfam	PF09019
Pfam clan	CL0236
InterPro	IPR015109
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

The apo crystal structure of EcoRII mutant R88A (PDB: 1NA6​)^[6] has been solved at 2.1 Å resolution. The EcoRII monomer has two domains, N-terminal and C-terminal, linked through a hinge loop.

Effector-binding domain

The N-terminal effector-binding domain has an archetypal DNA-binding pseudobarrel fold (SCOP 101936) with a prominent cleft. Structural superposition showed it is evolutionarily related to:

• B3 DNA binding domain (SCOP 117343) from the transcription factors in higher plants (PDB: 1WID​)^[7]
• C-terminal domain of restriction endonuclease BfiI^[8] (PDB: 2C1L​)^[9]

Catalytic domain

The C-terminal catalytic domain has a typical^[10] restriction endonuclease-like fold (SCOP 52979) and belongs to the large (more than 30 members) restriction endonuclease superfamily (SCOP 52980).

Autoinhibition/activation mechanism

Structure-based sequence alignment and site-directed mutagenesis identified the putative PD..D/EXK active sites of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.^[6]

See also

• EcoRI, another nuclease enzyme from Escherichia coli.
• EcoRV, another nuclease enzyme from Escherichia coli.
• B3 DNA binding domain from higher plants is evolutionary related to EcoRII
• FokI, another nuclease enzyme from Flavobacterium okeanokoites

External links

• EcoRII in Restriction Enzyme Database REBASE